[gmx-users] gmx distance

rose rahmani rose.rhmn93 at gmail.com
Sat Oct 6 15:55:53 CEST 2018


I have 30 similar amino acid around nanotune and i want to calculate the
average distance of all of them(i put all of AA in group of Protein in
index file and define them as 30 chain of protein means i have defined them
as Protein, Protein2, Protein3,...Protein30 in topol.top ) from
(infinite)NT during simulation. i used g_dist but as you now it calculates
COM distance of Protein and NT. but the COM of NT is just one point in the
NT so g_dist calculate the distance between COM of Protein and NT.(if
protein was closer to beginning of NT the distance(that g_dist show) will
be much different from when it's in middle part of NT( because at this time
Protein is maybe at the top of COM of NT,... )). but i want the distance
between Zaxis of NT to average distance of Protein(which is coleceted of 30
similar amino acids). So what should i do? i refer you to this picture(top).

Would you please help me?


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